[gmx-users] Osmotic pressure calculation, regarding

[RAHUL SURESH]

Hi Users.

I have done a protein-ligand simulation in POPC bilayer using charmm ff for
1000ns. How to calculate the osmotic pressure as well as the lateral
pressure of the system? If possible then Is it possible to do
post-simulation?



-- 
*Regards,*
*Rahul *
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[gmx-users] Osmotic pressure calculation

[RAHUL SURESH]

Hi Users.

I have done a protein-ligand simulation in POPC bilayer using charmm ff for
1000ns. I want to calculate the osmotic pressure as well as the lateral
pressure of the system. Is it possible to do post simulation?

Lateral pressure calculation like i want to slice the box and get the
pressure along Z direction.



-- 
*Regards,*
*Rahul *
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Re: [gmx-users] Osmotic Pressure Calculations and fixed reference values

[Mandar Kulkarni]

Dear Dr. Justin,
Thanks for the clarification and sorry for the delayed response from my
side.
I am calculating flat bottom potential along with osmotic pressure values
to verify my calculations. The flat bottom potential values calculated by
in-house code matches with g_energy values.
Thanks again.


On Dec 28, 2017 4:39 AM, 
wrote:

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Today's Topics:

   1. dielectric constant effect on protein, dna,   water interface
  (Sarath Chandra)
   2. More dihedrals generated than provided in the force field &
  "No default Proper Dih. types" as a result (Timofey Tyugashev)
   3. Re: More dihedrals generated than provided in the force field
  & "No default Proper Dih. types" as a result (Justin Lemkul)
   4. Re: regarding calculation of intra-residue energy (Justin Lemkul)
   5. Re: Osmotic Pressure Calculations and fixed reference values
  of walls (Justin Lemkul)
   6. Strange energy values with GMX 5.1, PME and Verlet (Diana Lousa)


--

Message: 1
Date: Wed, 27 Dec 2017 18:00:36 +0530
From: Sarath Chandra 
To: Discussion list for GROMACS users 
Subject: [gmx-users] dielectric constant effect on protein, dna,
water
interface
Message-ID:

Re: [gmx-users] Osmotic Pressure Calculations and fixed reference values of walls

[Justin Lemkul]

On 12/26/17 7:53 AM, Mandar Kulkarni wrote:

Dear All,
I am performing osmotic pressure simulations using 30 nucleoside molecules
using 1D flat bottom restraints along Z-axis(Zmin and Zmax). I am using
GROMACS 5.0.7 version and reference coordinates are provided using -r
option in grompp.
The osmotic pressure runs are performed under NPT conditions with
semi-isotropic pressure coupling. I am calculating osmotic pressure using
C-program which simply calculates forces on heavy atoms of nucleosides
attempting to cross the Zmin and Zmax limits.

I have searched archived posts, however, I am confused about possible
implementation and post-processing in the present case. Any help will be
really helpful to solve the following issues.

1. The upper and lower limits of the flat bottom restraints are defined
while starting the simulations using static reference frame. Although
|Zmax-Zmin|
will be constant, is it correct to assume fixed minimum(Zmin) and
maximum(Zmax) limits?


Such calculations are usually performed with a static z-dimension, e.g 
incompressible along that axis. In that case, Zmin and Zmax are (and 
should be) fixed.



2. During post-processing when one centers the trajectory and correct PBC
for nucleoside molecules (trjconv -pbc mol -ur compact -center options), is
it appropriate to assume the same Zmin and Zmax values at t=0 throughout
the analysis?


You shouldn't have to use any complex trjconv command. Just make 
molecules whole and that should be correct. No additional centering is 
required; your molecules stay in the central volume anyway, and you 
don't want to shift coordinates when relying on fixed points in space 
for computing your osmotic pressure forces.


-Justin


3. The GROMACS source code section below calculates flat-bottom restraint
forces

  for (m = 0; (m < DIM); m++)
 {
 f[ai][m]   += fm[m];
 /* Here we correct for the pbc_dx which included rdist */
 vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];

 }

How can we print force f[ai][m] at each time step to separate file? I
assume it might be not straightforward to print these forces, but a short
general guideline might help me to achieve the objective.

Sorry for so many questions and Thanks in advance.
Also, Wish you all happy new year in advance.

Best Regards,
Mandar Kulkarni,
Pusan National University, South Korea


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Osmotic Pressure Calculations and fixed reference values of walls

[Mandar Kulkarni]

Dear All,
I am performing osmotic pressure simulations using 30 nucleoside molecules
using 1D flat bottom restraints along Z-axis(Zmin and Zmax). I am using
GROMACS 5.0.7 version and reference coordinates are provided using -r
option in grompp.
The osmotic pressure runs are performed under NPT conditions with
semi-isotropic pressure coupling. I am calculating osmotic pressure using
C-program which simply calculates forces on heavy atoms of nucleosides
attempting to cross the Zmin and Zmax limits.

I have searched archived posts, however, I am confused about possible
implementation and post-processing in the present case. Any help will be
really helpful to solve the following issues.

1. The upper and lower limits of the flat bottom restraints are defined
while starting the simulations using static reference frame. Although
|Zmax-Zmin|
will be constant, is it correct to assume fixed minimum(Zmin) and
maximum(Zmax) limits?

2. During post-processing when one centers the trajectory and correct PBC
for nucleoside molecules (trjconv -pbc mol -ur compact -center options), is
it appropriate to assume the same Zmin and Zmax values at t=0 throughout
the analysis?

3. The GROMACS source code section below calculates flat-bottom restraint
forces

 for (m = 0; (m < DIM); m++)
{
f[ai][m]   += fm[m];
/* Here we correct for the pbc_dx which included rdist */
vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];

}

How can we print force f[ai][m] at each time step to separate file? I
assume it might be not straightforward to print these forces, but a short
general guideline might help me to achieve the objective.

Sorry for so many questions and Thanks in advance.
Also, Wish you all happy new year in advance.

Best Regards,
Mandar Kulkarni,
Pusan National University, South Korea
-- 
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Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hey Justin, 

These result was with Parinello-Rahman.
Here is the  setting for T and P coupling;

; Temperature coupling
tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Parrinello-Rahman   
pcoupltype  = semiisotropic 
tau_p   = 2.0 2.0 
ref_p   = 150.0 1.0 
compressibility = 0 4.5e-5
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= no   

> On 18 Apr 2016, at 15:48, Justin Lemkul  wrote:
> 
> 
> 
> On 4/18/16 4:43 AM, gozde ergin wrote:
>> In Roux study they did 10 independent 1.5 ns production simulation and I did 
>> 15 ns simulation and divided it to 10 1.5ns simulations.
>> 
>> Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
>>   Roux study 300(+/- 10  bar)
>>   Experiment 300 bar
> 
> Your fluctuation seems unreasonably low.  Is this still with Berendsen?  If 
> so, repeat it using Parrinello-Rahman for the barostat.  This result should 
> be quite reproducible when using the method described exactly in the paper.
> 
> -Justin

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Re: [gmx-users] Osmotic pressure

[Justin Lemkul]

On 4/18/16 4:43 AM, gozde ergin wrote:

In Roux study they did 10 independent 1.5 ns production simulation and I did 15 
ns simulation and divided it to 10 1.5ns simulations.

Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
   Roux study 300(+/- 10  bar)
   Experiment 300 bar


Your fluctuation seems unreasonably low.  Is this still with Berendsen?  If so, 
repeat it using Parrinello-Rahman for the barostat.  This result should be quite 
reproducible when using the method described exactly in the paper.


-Justin


On 18 Apr 2016, at 10:29, Mark Abraham  wrote:

Hi,

What statistical error do you (and they) measure? How many replicates have
each of you done?

Mark

On Mon, 18 Apr 2016 10:25 gozde ergin  wrote:


Hi Justin,

I corrected the nonbonded settings as your suggestion ;

; Bond parameters
continuation = no
constraint_algorithm = shake
constraints  = h-bonds
shake_tol= 0.0001
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
; Neighborsearching
ns_type = grid
nstlist = 5
rlist   = 1.2
rcoulomb= 1.2
rvdw= 1.2

However my osmotic pressure result is still far from the Luo 2010
study.
I have the same number of Na Cl ions and water molecules. I run the
simulation for 15ns.
System size is the same, water model and force field are the same as Roux
study.
Basically I should get the same result.
Here is the result,

Osmotic pressure for 5M : My result 217 bar
  Roux study ~300 bar

Any suggestions would be appreciated.


On 15 Apr 2016, at 11:50, Justin Lemkul  wrote:



On 4/15/16 5:20 AM, gozde ergin wrote:

Dear all,

I simulate the NaCl solution to estimate the osmotic pressure. My salt

concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
molecules.

I use CHARMM36 ff with NBFIX correction.

After the simulation I extract the z-coordinates of restraint ions and

use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
pressure.

Actually I try to get the similar results as Lou 2010 study.

However my osmotic pressure results are on the line of ideal solution

osmotic pressure as shown equation in below;


P = cRT (Van’t Hoff equation)

but not the similar result with experiments.



What values do you actually get?  How do they compare with the values

from the Roux paper?  Are you remembering to divide by 2*area in your
calculation (since you have two walls)?



Is there anyone here that get the same trend as me for osmotic pressure

calculation? Or is there something that I miss?



Here is my .mdp file;

define   = -DPOSRES
integrator   = md
dt   = 0.002
nsteps   = 250   ;
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no;
constraint_algorithm = shake ; h
constraints  = all-bonds ; a
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ;
nstlist = 5 ;
rlist   = 1.1   ;
rcoulomb= 1.1   ;
rvdw= 1.1   ;


These nonbonded settings are wrong.  The values for CHARMM36 are well

established and you should not deviate from them.


http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM <

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM>


-Justin


; Electrostatics
coulombtype = PME   ;
pme_order   = 4 ;
fourierspacing  = 0.16  ;

tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also

weak coupling

pcoupltype  = semiisotropic ; uniform scaling of x-y-z box

vectors

tau_p   = 2.0 2.0  ; time constant, in ps
ref_p   = 1.0 1.0  ; reference pressure (in bar)
compressibility = 0 4.5e-5; isothermal compressibility,

bar^-1

refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hi Mark,

I guess so because a lot of studies cite this study also their results are 
almost identical with the experimental one.

> On 18 Apr 2016, at 10:46, Mark Abraham  wrote:
> 
> Are they known to produce these observables accurately

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Re: [gmx-users] Osmotic pressure

[Mark Abraham]

Hi,

Are they known to produce these observables accurately? Might a wrong
distribution of KE affect them?

Mark

On Fri, 15 Apr 2016 12:00 gozde ergin  wrote:

> Hi Mark,
>
> I use Berendsen for T and P-coupl.
> Do you think I should change them?
>
> > On 15 Apr 2016, at 11:55, Mark Abraham  wrote:
> >
> > Hi,
> >
> > Also you can choose coupling algorithms that are known to sample correct
> > ensembles...
> >
> > Mark
> >
> > On Fri, 15 Apr 2016 11:50 Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 4/15/16 5:20 AM, gozde ergin wrote:
> >>> Dear all,
> >>>
> >>> I simulate the NaCl solution to estimate the osmotic pressure. My salt
> >> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
> >> molecules.
> >>> I use CHARMM36 ff with NBFIX correction.
> >>>
> >>> After the simulation I extract the z-coordinates of restraint ions and
> >> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the
> osmotic
> >> pressure.
> >>> Actually I try to get the similar results as Lou 2010 study.
> >>>
> >>> However my osmotic pressure results are on the line of ideal solution
> >> osmotic pressure as shown equation in below;
> >>>
> >>> P = cRT (Van’t Hoff equation)
> >>>
> >>> but not the similar result with experiments.
> >>>
> >>
> >> What values do you actually get?  How do they compare with the values
> from
> >> the
> >> Roux paper?  Are you remembering to divide by 2*area in your calculation
> >> (since
> >> you have two walls)?
> >>
> >>> Is there anyone here that get the same trend as me for osmotic pressure
> >> calculation? Or is there something that I miss?
> >>>
> >>>
> >>> Here is my .mdp file;
> >>>
> >>> define   = -DPOSRES
> >>> integrator   = md
> >>> dt   = 0.002
> >>> nsteps   = 250   ;
> >>> ; Output control
> >>> nstxout  = 2000
> >>> nstvout  = 2000
> >>> nstlog   = 2000
> >>> nstenergy= 2000
> >>> ; Bond parameters
> >>> continuation = no;
> >>> constraint_algorithm = shake ; h
> >>> constraints  = all-bonds ; a
> >>> shake_tol= 0.0001
> >>> ; Neighborsearching
> >>> ns_type = grid  ;
> >>> nstlist = 5 ;
> >>> rlist   = 1.1   ;
> >>> rcoulomb= 1.1   ;
> >>> rvdw= 1.1   ;
> >>
> >> These nonbonded settings are wrong.  The values for CHARMM36 are well
> >> established and you should not deviate from them.
> >>
> >> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
> >>
> >> -Justin
> >>
> >>> ; Electrostatics
> >>> coulombtype = PME   ;
> >>> pme_order   = 4 ;
> >>> fourierspacing  = 0.16  ;
> >>>
> >>> tcoupl   = berendsen
> >>> tc-grps  = System
> >>> tau_t= 1.0
> >>> ref_t= 300
> >>> ; Pressure coupling is on
> >>> pcoupl  = Berendsen ; Pressure coupling on in NPT, also
> >> weak coupling
> >>> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
> >> vectors
> >>> tau_p   = 2.0 2.0  ; time constant, in ps
> >>> ref_p   = 1.0 1.0  ; reference pressure (in bar)
> >>> compressibility = 0 4.5e-5; isothermal compressibility,
> >> bar^-1
> >>> refcoord_scaling= com
> >>> ; Periodic boundary conditions
> >>> pbc = xyz   ; 3-D PBC
> >>> ; Dispersion correction
> >>> DispCorr= EnerPres  ; account for cut-off vdW scheme
> >>> ; Velocity generation
> >>> gen_vel = yes   ; Velocity generation is on
> >>> gen_temp= 300   ; temperature for velocity generation
> >>> gen_seed= -1; random seed
> >>> ; COM motion removal
> >>> ; These options remove COM motion of the system
> >>> nstcomm = 10
> >>> comm-mode   = Linear
> >>> comm-grps   = System
> >>>
> >>>
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to 

Re: [gmx-users] Osmotic pressure

[gozde ergin]

In Roux study they did 10 independent 1.5 ns production simulation and I did 15 
ns simulation and divided it to 10 1.5ns simulations.

Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
  Roux study 300(+/- 10  bar)
  Experiment 300 bar
> On 18 Apr 2016, at 10:29, Mark Abraham  wrote:
> 
> Hi,
> 
> What statistical error do you (and they) measure? How many replicates have
> each of you done?
> 
> Mark
> 
> On Mon, 18 Apr 2016 10:25 gozde ergin  wrote:
> 
>> Hi Justin,
>> 
>> I corrected the nonbonded settings as your suggestion ;
>> 
>> ; Bond parameters
>> continuation = no
>> constraint_algorithm = shake
>> constraints  = h-bonds
>> shake_tol= 0.0001
>> cutoff-scheme = Verlet
>> vdwtype = cutoff
>> vdw-modifier = force-switch
>> rvdw-switch = 1.0
>> ; Neighborsearching
>> ns_type = grid
>> nstlist = 5
>> rlist   = 1.2
>> rcoulomb= 1.2
>> rvdw= 1.2
>> 
>> However my osmotic pressure result is still far from the Luo 2010
>> study.
>> I have the same number of Na Cl ions and water molecules. I run the
>> simulation for 15ns.
>> System size is the same, water model and force field are the same as Roux
>> study.
>> Basically I should get the same result.
>> Here is the result,
>> 
>> Osmotic pressure for 5M : My result 217 bar
>>  Roux study ~300 bar
>> 
>> Any suggestions would be appreciated.
>> 
>>> On 15 Apr 2016, at 11:50, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 4/15/16 5:20 AM, gozde ergin wrote:
 Dear all,
 
 I simulate the NaCl solution to estimate the osmotic pressure. My salt
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
>> molecules.
 I use CHARMM36 ff with NBFIX correction.
 
 After the simulation I extract the z-coordinates of restraint ions and
>> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
>> pressure.
 Actually I try to get the similar results as Lou 2010 study.
 
 However my osmotic pressure results are on the line of ideal solution
>> osmotic pressure as shown equation in below;
 
 P = cRT (Van’t Hoff equation)
 
 but not the similar result with experiments.
 
>>> 
>>> What values do you actually get?  How do they compare with the values
>> from the Roux paper?  Are you remembering to divide by 2*area in your
>> calculation (since you have two walls)?
>>> 
 Is there anyone here that get the same trend as me for osmotic pressure
>> calculation? Or is there something that I miss?
 
 
 Here is my .mdp file;
 
 define   = -DPOSRES
 integrator   = md
 dt   = 0.002
 nsteps   = 250   ;
 ; Output control
 nstxout  = 2000
 nstvout  = 2000
 nstlog   = 2000
 nstenergy= 2000
 ; Bond parameters
 continuation = no;
 constraint_algorithm = shake ; h
 constraints  = all-bonds ; a
 shake_tol= 0.0001
 ; Neighborsearching
 ns_type = grid  ;
 nstlist = 5 ;
 rlist   = 1.1   ;
 rcoulomb= 1.1   ;
 rvdw= 1.1   ;
>>> 
>>> These nonbonded settings are wrong.  The values for CHARMM36 are well
>> established and you should not deviate from them.
>>> 
>>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM <
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM>
>>> 
>>> -Justin
>>> 
 ; Electrostatics
 coulombtype = PME   ;
 pme_order   = 4 ;
 fourierspacing  = 0.16  ;
 
 tcoupl   = berendsen
 tc-grps  = System
 tau_t= 1.0
 ref_t= 300
 ; Pressure coupling is on
 pcoupl  = Berendsen ; Pressure coupling on in NPT, also
>> weak coupling
 pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
>> vectors
 tau_p   = 2.0 2.0  ; time constant, in ps
 ref_p   = 1.0 1.0  ; reference pressure (in bar)
 compressibility = 0 4.5e-5; isothermal compressibility,
>> bar^-1
 refcoord_scaling= com
 ; Periodic boundary conditions
 pbc = xyz   ; 3-D PBC
 ; Dispersion correction
 DispCorr= EnerPres  ; account for cut-off vdW scheme
 ; Velocity generation
 gen_vel = yes   ; Velocity generation is on
 gen_temp= 300   ; temperature for velocity generation
 gen_seed= -1; random seed
 ; COM motion removal
 ; These options 

Re: [gmx-users] Osmotic pressure

[Mark Abraham]

Hi,

What statistical error do you (and they) measure? How many replicates have
each of you done?

Mark

On Mon, 18 Apr 2016 10:25 gozde ergin  wrote:

> Hi Justin,
>
> I corrected the nonbonded settings as your suggestion ;
>
> ; Bond parameters
> continuation = no
> constraint_algorithm = shake
> constraints  = h-bonds
> shake_tol= 0.0001
> cutoff-scheme = Verlet
> vdwtype = cutoff
> vdw-modifier = force-switch
> rvdw-switch = 1.0
> ; Neighborsearching
> ns_type = grid
> nstlist = 5
> rlist   = 1.2
> rcoulomb= 1.2
> rvdw= 1.2
>
> However my osmotic pressure result is still far from the Luo 2010
> study.
> I have the same number of Na Cl ions and water molecules. I run the
> simulation for 15ns.
> System size is the same, water model and force field are the same as Roux
> study.
> Basically I should get the same result.
> Here is the result,
>
> Osmotic pressure for 5M : My result 217 bar
>   Roux study ~300 bar
>
> Any suggestions would be appreciated.
>
> > On 15 Apr 2016, at 11:50, Justin Lemkul  wrote:
> >
> >
> >
> > On 4/15/16 5:20 AM, gozde ergin wrote:
> >> Dear all,
> >>
> >> I simulate the NaCl solution to estimate the osmotic pressure. My salt
> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
> molecules.
> >> I use CHARMM36 ff with NBFIX correction.
> >>
> >> After the simulation I extract the z-coordinates of restraint ions and
> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
> pressure.
> >> Actually I try to get the similar results as Lou 2010 study.
> >>
> >> However my osmotic pressure results are on the line of ideal solution
> osmotic pressure as shown equation in below;
> >>
> >> P = cRT (Van’t Hoff equation)
> >>
> >> but not the similar result with experiments.
> >>
> >
> > What values do you actually get?  How do they compare with the values
> from the Roux paper?  Are you remembering to divide by 2*area in your
> calculation (since you have two walls)?
> >
> >> Is there anyone here that get the same trend as me for osmotic pressure
> calculation? Or is there something that I miss?
> >>
> >>
> >> Here is my .mdp file;
> >>
> >> define   = -DPOSRES
> >> integrator   = md
> >> dt   = 0.002
> >> nsteps   = 250   ;
> >> ; Output control
> >> nstxout  = 2000
> >> nstvout  = 2000
> >> nstlog   = 2000
> >> nstenergy= 2000
> >> ; Bond parameters
> >> continuation = no;
> >> constraint_algorithm = shake ; h
> >> constraints  = all-bonds ; a
> >> shake_tol= 0.0001
> >> ; Neighborsearching
> >> ns_type = grid  ;
> >> nstlist = 5 ;
> >> rlist   = 1.1   ;
> >> rcoulomb= 1.1   ;
> >> rvdw= 1.1   ;
> >
> > These nonbonded settings are wrong.  The values for CHARMM36 are well
> established and you should not deviate from them.
> >
> > http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM <
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM>
> >
> > -Justin
> >
> >> ; Electrostatics
> >> coulombtype = PME   ;
> >> pme_order   = 4 ;
> >> fourierspacing  = 0.16  ;
> >>
> >> tcoupl   = berendsen
> >> tc-grps  = System
> >> tau_t= 1.0
> >> ref_t= 300
> >> ; Pressure coupling is on
> >> pcoupl  = Berendsen ; Pressure coupling on in NPT, also
> weak coupling
> >> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
> vectors
> >> tau_p   = 2.0 2.0  ; time constant, in ps
> >> ref_p   = 1.0 1.0  ; reference pressure (in bar)
> >> compressibility = 0 4.5e-5; isothermal compressibility,
> bar^-1
> >> refcoord_scaling= com
> >> ; Periodic boundary conditions
> >> pbc = xyz   ; 3-D PBC
> >> ; Dispersion correction
> >> DispCorr= EnerPres  ; account for cut-off vdW scheme
> >> ; Velocity generation
> >> gen_vel = yes   ; Velocity generation is on
> >> gen_temp= 300   ; temperature for velocity generation
> >> gen_seed= -1; random seed
> >> ; COM motion removal
> >> ; These options remove COM motion of the system
> >> nstcomm = 10
> >> comm-mode   = Linear
> >> comm-grps   = System
> >>
> >>
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > 

Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hi Justin,

I corrected the nonbonded settings as your suggestion ; 

; Bond parameters
continuation = no   
constraint_algorithm = shake 
constraints  = h-bonds 
shake_tol= 0.0001
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
; Neighborsearching
ns_type = grid
nstlist = 5 
rlist   = 1.2   
rcoulomb= 1.2 
rvdw= 1.2  

However my osmotic pressure result is still far from the Luo 2010 study.
I have the same number of Na Cl ions and water molecules. I run the simulation 
for 15ns.
System size is the same, water model and force field are the same as Roux 
study. 
Basically I should get the same result.
Here is the result,

Osmotic pressure for 5M : My result 217 bar
  Roux study ~300 bar

Any suggestions would be appreciated.

> On 15 Apr 2016, at 11:50, Justin Lemkul  wrote:
> 
> 
> 
> On 4/15/16 5:20 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I simulate the NaCl solution to estimate the osmotic pressure. My salt 
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the 
>> molecules.
>> I use CHARMM36 ff with NBFIX correction.
>> 
>> After the simulation I extract the z-coordinates of restraint ions and use 
>> the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic 
>> pressure.
>> Actually I try to get the similar results as Lou 2010 study.
>> 
>> However my osmotic pressure results are on the line of ideal solution 
>> osmotic pressure as shown equation in below;
>> 
>> P = cRT (Van’t Hoff equation)
>> 
>> but not the similar result with experiments.
>> 
> 
> What values do you actually get?  How do they compare with the values from 
> the Roux paper?  Are you remembering to divide by 2*area in your calculation 
> (since you have two walls)?
> 
>> Is there anyone here that get the same trend as me for osmotic pressure 
>> calculation? Or is there something that I miss?
>> 
>> 
>> Here is my .mdp file;
>> 
>> define   = -DPOSRES
>> integrator   = md
>> dt   = 0.002
>> nsteps   = 250   ;
>> ; Output control
>> nstxout  = 2000
>> nstvout  = 2000
>> nstlog   = 2000
>> nstenergy= 2000
>> ; Bond parameters
>> continuation = no;
>> constraint_algorithm = shake ; h
>> constraints  = all-bonds ; a
>> shake_tol= 0.0001
>> ; Neighborsearching
>> ns_type = grid  ;
>> nstlist = 5 ;
>> rlist   = 1.1   ;
>> rcoulomb= 1.1   ;
>> rvdw= 1.1   ;
> 
> These nonbonded settings are wrong.  The values for CHARMM36 are well 
> established and you should not deviate from them.
> 
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM 
> 
> 
> -Justin
> 
>> ; Electrostatics
>> coulombtype = PME   ;
>> pme_order   = 4 ;
>> fourierspacing  = 0.16  ;
>> 
>> tcoupl   = berendsen
>> tc-grps  = System
>> tau_t= 1.0
>> ref_t= 300
>> ; Pressure coupling is on
>> pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
>> coupling
>> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box 
>> vectors
>> tau_p   = 2.0 2.0  ; time constant, in ps
>> ref_p   = 1.0 1.0  ; reference pressure (in bar)
>> compressibility = 0 4.5e-5; isothermal compressibility, bar^-1
>> refcoord_scaling= com
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; Velocity generation is on
>> gen_temp= 300   ; temperature for velocity generation
>> gen_seed= -1; random seed
>> ; COM motion removal
>> ; These options remove COM motion of the system
>> nstcomm = 10
>> comm-mode   = Linear
>> comm-grps   = System
>> 
>> 
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu  
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> 
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> 

Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hi Mark,

I use Berendsen for T and P-coupl.
Do you think I should change them?

> On 15 Apr 2016, at 11:55, Mark Abraham  wrote:
> 
> Hi,
> 
> Also you can choose coupling algorithms that are known to sample correct
> ensembles...
> 
> Mark
> 
> On Fri, 15 Apr 2016 11:50 Justin Lemkul  wrote:
> 
>> 
>> 
>> On 4/15/16 5:20 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I simulate the NaCl solution to estimate the osmotic pressure. My salt
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
>> molecules.
>>> I use CHARMM36 ff with NBFIX correction.
>>> 
>>> After the simulation I extract the z-coordinates of restraint ions and
>> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
>> pressure.
>>> Actually I try to get the similar results as Lou 2010 study.
>>> 
>>> However my osmotic pressure results are on the line of ideal solution
>> osmotic pressure as shown equation in below;
>>> 
>>> P = cRT (Van’t Hoff equation)
>>> 
>>> but not the similar result with experiments.
>>> 
>> 
>> What values do you actually get?  How do they compare with the values from
>> the
>> Roux paper?  Are you remembering to divide by 2*area in your calculation
>> (since
>> you have two walls)?
>> 
>>> Is there anyone here that get the same trend as me for osmotic pressure
>> calculation? Or is there something that I miss?
>>> 
>>> 
>>> Here is my .mdp file;
>>> 
>>> define   = -DPOSRES
>>> integrator   = md
>>> dt   = 0.002
>>> nsteps   = 250   ;
>>> ; Output control
>>> nstxout  = 2000
>>> nstvout  = 2000
>>> nstlog   = 2000
>>> nstenergy= 2000
>>> ; Bond parameters
>>> continuation = no;
>>> constraint_algorithm = shake ; h
>>> constraints  = all-bonds ; a
>>> shake_tol= 0.0001
>>> ; Neighborsearching
>>> ns_type = grid  ;
>>> nstlist = 5 ;
>>> rlist   = 1.1   ;
>>> rcoulomb= 1.1   ;
>>> rvdw= 1.1   ;
>> 
>> These nonbonded settings are wrong.  The values for CHARMM36 are well
>> established and you should not deviate from them.
>> 
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>> 
>> -Justin
>> 
>>> ; Electrostatics
>>> coulombtype = PME   ;
>>> pme_order   = 4 ;
>>> fourierspacing  = 0.16  ;
>>> 
>>> tcoupl   = berendsen
>>> tc-grps  = System
>>> tau_t= 1.0
>>> ref_t= 300
>>> ; Pressure coupling is on
>>> pcoupl  = Berendsen ; Pressure coupling on in NPT, also
>> weak coupling
>>> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
>> vectors
>>> tau_p   = 2.0 2.0  ; time constant, in ps
>>> ref_p   = 1.0 1.0  ; reference pressure (in bar)
>>> compressibility = 0 4.5e-5; isothermal compressibility,
>> bar^-1
>>> refcoord_scaling= com
>>> ; Periodic boundary conditions
>>> pbc = xyz   ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel = yes   ; Velocity generation is on
>>> gen_temp= 300   ; temperature for velocity generation
>>> gen_seed= -1; random seed
>>> ; COM motion removal
>>> ; These options remove COM motion of the system
>>> nstcomm = 10
>>> comm-mode   = Linear
>>> comm-grps   = System
>>> 
>>> 
>> 
>> --
>> ==
>> 
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> 
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> 
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> 
>> ==
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
> -- 
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> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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* Please search 

Re: [gmx-users] Osmotic pressure

[Mark Abraham]

Hi,

Also you can choose coupling algorithms that are known to sample correct
ensembles...

Mark

On Fri, 15 Apr 2016 11:50 Justin Lemkul  wrote:

>
>
> On 4/15/16 5:20 AM, gozde ergin wrote:
> > Dear all,
> >
> > I simulate the NaCl solution to estimate the osmotic pressure. My salt
> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
> molecules.
> > I use CHARMM36 ff with NBFIX correction.
> >
> > After the simulation I extract the z-coordinates of restraint ions and
> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
> pressure.
> > Actually I try to get the similar results as Lou 2010 study.
> >
> > However my osmotic pressure results are on the line of ideal solution
> osmotic pressure as shown equation in below;
> >
> > P = cRT (Van’t Hoff equation)
> >
> > but not the similar result with experiments.
> >
>
> What values do you actually get?  How do they compare with the values from
> the
> Roux paper?  Are you remembering to divide by 2*area in your calculation
> (since
> you have two walls)?
>
> > Is there anyone here that get the same trend as me for osmotic pressure
> calculation? Or is there something that I miss?
> >
> >
> > Here is my .mdp file;
> >
> > define   = -DPOSRES
> > integrator   = md
> > dt   = 0.002
> > nsteps   = 250   ;
> > ; Output control
> > nstxout  = 2000
> > nstvout  = 2000
> > nstlog   = 2000
> > nstenergy= 2000
> > ; Bond parameters
> > continuation = no;
> > constraint_algorithm = shake ; h
> > constraints  = all-bonds ; a
> > shake_tol= 0.0001
> > ; Neighborsearching
> > ns_type = grid  ;
> > nstlist = 5 ;
> > rlist   = 1.1   ;
> > rcoulomb= 1.1   ;
> > rvdw= 1.1   ;
>
> These nonbonded settings are wrong.  The values for CHARMM36 are well
> established and you should not deviate from them.
>
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> -Justin
>
> > ; Electrostatics
> > coulombtype = PME   ;
> > pme_order   = 4 ;
> > fourierspacing  = 0.16  ;
> >
> > tcoupl   = berendsen
> > tc-grps  = System
> > tau_t= 1.0
> > ref_t= 300
> > ; Pressure coupling is on
> > pcoupl  = Berendsen ; Pressure coupling on in NPT, also
> weak coupling
> > pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
> vectors
> > tau_p   = 2.0 2.0  ; time constant, in ps
> > ref_p   = 1.0 1.0  ; reference pressure (in bar)
> > compressibility = 0 4.5e-5; isothermal compressibility,
> bar^-1
> > refcoord_scaling= com
> > ; Periodic boundary conditions
> > pbc = xyz   ; 3-D PBC
> > ; Dispersion correction
> > DispCorr= EnerPres  ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = yes   ; Velocity generation is on
> > gen_temp= 300   ; temperature for velocity generation
> > gen_seed= -1; random seed
> > ; COM motion removal
> > ; These options remove COM motion of the system
> > nstcomm = 10
> > comm-mode   = Linear
> > comm-grps   = System
> >
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Osmotic pressure

[Justin Lemkul]

On 4/15/16 5:20 AM, gozde ergin wrote:

Dear all,

I simulate the NaCl solution to estimate the osmotic pressure. My salt 
concentrations are 3,4 and 5M. I apply flat-bottom restraint to the molecules.
I use CHARMM36 ff with NBFIX correction.

After the simulation I extract the z-coordinates of restraint ions and use the 
equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic pressure.
Actually I try to get the similar results as Lou 2010 study.

However my osmotic pressure results are on the line of ideal solution osmotic 
pressure as shown equation in below;

P = cRT (Van’t Hoff equation)

but not the similar result with experiments.



What values do you actually get?  How do they compare with the values from the 
Roux paper?  Are you remembering to divide by 2*area in your calculation (since 
you have two walls)?



Is there anyone here that get the same trend as me for osmotic pressure 
calculation? Or is there something that I miss?


Here is my .mdp file;

define   = -DPOSRES
integrator   = md
dt   = 0.002
nsteps   = 250   ;
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no;
constraint_algorithm = shake ; h
constraints  = all-bonds ; a
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ;
nstlist = 5 ;
rlist   = 1.1   ;
rcoulomb= 1.1   ;
rvdw= 1.1   ;


These nonbonded settings are wrong.  The values for CHARMM36 are well 
established and you should not deviate from them.


http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

-Justin


; Electrostatics
coulombtype = PME   ;
pme_order   = 4 ;
fourierspacing  = 0.16  ;

tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
coupling
pcoupltype  = semiisotropic ; uniform scaling of x-y-z box vectors
tau_p   = 2.0 2.0  ; time constant, in ps
ref_p   = 1.0 1.0  ; reference pressure (in bar)
compressibility = 0 4.5e-5; isothermal compressibility, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Osmotic pressure

[gozde ergin]

Dear all,

I simulate the NaCl solution to estimate the osmotic pressure. My salt 
concentrations are 3,4 and 5M. I apply flat-bottom restraint to the molecules.
I use CHARMM36 ff with NBFIX correction.

After the simulation I extract the z-coordinates of restraint ions and use the 
equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic pressure.
Actually I try to get the similar results as Lou 2010 study.

However my osmotic pressure results are on the line of ideal solution osmotic 
pressure as shown equation in below; 

P = cRT (Van’t Hoff equation) 

but not the similar result with experiments. 

Is there anyone here that get the same trend as me for osmotic pressure 
calculation? Or is there something that I miss?


Here is my .mdp file;

define   = -DPOSRES
integrator   = md 
dt   = 0.002
nsteps   = 250   ; 
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no; 
constraint_algorithm = shake ; h
constraints  = all-bonds ; a
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ; 
nstlist = 5 ; 
rlist   = 1.1   ; 
rcoulomb= 1.1   ; 
rvdw= 1.1   ; 
; Electrostatics
coulombtype = PME   ; 
pme_order   = 4 ; 
fourierspacing  = 0.16  ; 

tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
coupling
pcoupltype  = semiisotropic ; uniform scaling of x-y-z box vectors
tau_p   = 2.0 2.0  ; time constant, in ps
ref_p   = 1.0 1.0  ; reference pressure (in bar)
compressibility = 0 4.5e-5; isothermal compressibility, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System 


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